Contacts of the helix formed by residues 342 - 348 (chain A) in PDB entry 3RSG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A ILE 3.1 10.3 + - - +
315A GLY* 3.2 9.4 - - - -
316A PRO* 3.9 13.3 - - + +
341A ILE* 1.3 73.6 - - - +
343A ALA* 1.3 87.9 + - + +
345A ALA* 2.9 15.2 + - - +
346A ILE* 3.4 7.2 + - - -
364A THR* 2.7 30.9 + - + +
369A GLU* 4.6 0.5 - - - +
402A LYS* 3.3 9.6 + - - -
430A GLY 3.9 7.8 - - - +
431A ASP* 4.3 4.7 - - - +
434A THR* 2.5 38.1 + - + +
492A MG 4.1 2.2 - - - -
494A APR 5.4 0.9 + - - +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A GLY 3.5 11.4 - - - +
316A PRO* 3.7 13.2 - - + -
317A GLY 4.6 1.3 - - - +
342A ASP* 1.3 88.4 + - - +
344A ASP* 1.3 62.0 + - - +
346A ILE* 2.8 29.0 + - - +
347A ASN* 3.0 14.8 + - - -
369A GLU* 3.3 21.1 + - - +
494A APR 3.6 24.7 - - - +
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A TYR* 4.6 5.9 - - - -
315A GLY 3.3 9.3 + - - +
317A GLY* 4.2 5.4 + - - -
318A LEU* 3.8 8.2 + - + -
319A GLY* 2.9 47.7 + - - +
320A ASN* 3.7 11.7 - - + +
343A ALA* 1.3 80.3 - - - +
345A ALA* 1.3 60.8 + - - +
347A ASN* 3.0 22.6 + - - +
348A VAL* 3.1 28.4 + - - +
494A APR 4.7 10.5 + - - -
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ILE* 3.4 37.7 - - + +
315A GLY* 3.5 10.5 - - - +
318A LEU* 4.7 0.4 - - - +
328A VAL* 4.0 18.8 - - + +
341A ILE* 3.8 16.7 - - + +
342A ASP 2.9 4.5 + - - +
344A ASP* 1.3 76.4 - - - +
346A ILE* 1.3 60.8 + - - +
348A VAL* 3.7 9.1 + - - +
349A LEU* 3.2 22.7 + - - +
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Residues in contact with ILE 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A ILE* 3.5 28.0 - - + +
342A ASP* 3.4 11.8 + - - -
343A ALA* 2.8 13.1 + - - +
345A ALA* 1.3 75.4 - - - +
347A ASN* 1.3 65.2 + - - +
349A LEU* 3.1 19.6 + - - +
363A LEU* 4.6 7.0 - - + -
364A THR 3.5 10.5 - - - +
365A PRO* 3.3 39.3 - - + -
369A GLU* 4.3 22.4 - - + +
373A LEU* 3.9 37.2 - - + +
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Residues in contact with ASN 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ASN* 4.0 20.8 + - - +
325A ARG* 4.0 10.2 + - - -
343A ALA 3.0 17.7 + - - -
344A ASP* 3.0 30.4 + - - +
346A ILE* 1.3 75.6 - - - +
348A VAL* 1.3 60.4 + - - +
349A LEU 5.1 0.3 - - - +
369A GLU* 3.6 18.1 + - - +
372A ARG* 2.3 41.2 + - - +
494A APR 5.4 2.6 + - - -
495A NAD 4.7 5.1 + - - -
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A ASN* 3.2 37.9 - - + +
321A ASN 4.5 0.2 - - - +
324A VAL* 4.4 3.6 - - + -
325A ARG* 3.3 56.6 + - + +
328A VAL* 3.8 26.5 - - + -
329A ASN* 3.0 16.5 + - - -
344A ASP 3.1 16.5 + - - +
345A ALA 3.9 2.7 - - - +
347A ASN* 1.3 78.6 - - - +
349A LEU* 1.3 67.0 + - - +
350A ASP* 4.9 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il